where does *.seave come from

3 files changed, 13 insertions, 239 deletions

diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index cb1c1a313..3761f4e1d 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -14,7 +14,6 @@ EBUILD ccp4-libs-6.1.1-r4.ebuild 5776 RMD160 3a36e4a2fff69e2a17028c39f8849a4cfd7
 EBUILD ccp4-libs-6.1.1-r6.ebuild 5956 RMD160 88f4d6e5c9067225501f214002bc5924bc07c1a2 SHA1 8e61890578007833d8a923eeada3bdf064354056 SHA256 1e7bde2c6f9319d699cf95565aa74bd26372b9d1275fdeaaa8ee75fb4001b30a
 EBUILD ccp4-libs-6.1.1-r7.ebuild 6093 RMD160 99176fde51fd41e7b29610a15720859e97b22d01 SHA1 6a52cfb8e4cddd9454db90bb90bad600c3b753ec SHA256 2143d0c1a7905107b9699cce41d7f33a6fedc99cf9046de33d7b42ddafdfa937
 EBUILD ccp4-libs-6.1.1.ebuild 5211 RMD160 6f3705f7ab0c48bbda073eb7dc1a283b3dcaa39a SHA1 8b09909daae034fc393b49b5fda7e06a783bcd14 SHA256 e9b4a3183a8f753ced59968b261bb655c87d13ade8c9964c71f1f2948c42067e
-EBUILD ccp4-libs-6.1.2.ebuild 6784 RMD160 785dc7bf1ca755b66ab6dad2d2e2a3efc0bfa76d SHA1 b6df87140bb72012ca88920c6ba9f36d5a50c033 SHA256 0cc19814e23e525bb74acc921f22c0c73f9fee522a5bf323259477e0a87c454c
+EBUILD ccp4-libs-6.1.2.ebuild 6315 RMD160 6f2aaf5168c4ab01bb4da8a9bce9deaa2f7fa165 SHA1 29a67d4e54baa80c91ac11e898db28713af93677 SHA256 8f105ffc4e670cfb868ea7dcbe984d40a6ad29d33fb545b2ce23d006829e654a
 MISC ChangeLog 2431 RMD160 35e051f578142a24e0c488bb79972b6ec03e8f53 SHA1 51c7326eaee4b4cec3d1f847ba92087ada731263 SHA256 df369e675d208c704403dd341ceb4ef57fb8a0e27760762cc59e6e4bce294d98
-MISC ccp4-libs-6.1.2.ebuild.save 6779 RMD160 b63cef13d5584d4318abfc2db3144c3e844316b0 SHA1 b3d2d68c38b8f4a57607d7010e5b6d9646cba1cc SHA256 b6078ff2f676f0538d3d0ed9bb260d9d5eacd98a95ee3e9f1997f845f53eb40a
 MISC metadata.xml 309 RMD160 b9d7f0a63f8fb51e9b4e2d6b4f4028541df5400c SHA1 26ee4b64e0e4d52b1afe00957d53b0cc2956da00 SHA256 04f156de856eae11c0cf8af213f74a9852213844cdd5133aa01dbe60371d57e7
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
index 59d82e597..c60851eaf 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
@@ -29,18 +29,22 @@ DESCRIPTION="Protein X-ray crystallography toolkit"
 HOMEPAGE="http://www.ccp4.ac.uk/"
 RESTRICT="mirror"
 SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-#	${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
-#	http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+# patch tarball from upstream
+	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+# patches created by us
+	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
 
 for i in $(seq $PATCH_TOT); do
 	NAME="PATCH${i}[1]"
 	SRC_URI="${SRC_URI}
 		${SRC}/${PV}/patches/${!NAME}"
 done
+
 LICENSE="ccp4"
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
+
 RDEPEND="virtual/lapack
 	virtual/blas
 	=sci-libs/fftw-2*
@@ -49,7 +53,7 @@ RDEPEND="virtual/lapack
 	sci-libs/monomer-db"
 DEPEND="${RDEPEND}"
 
-S="${WORKDIR}/${P/-libs}"
+S="${WORKDIR}/${MY_P}"
 
 src_unpack() {
 	unpack ${A}
@@ -67,7 +71,7 @@ src_unpack() {
 	einfo "Done."
 	echo
 
-#	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
 
 	einfo "Applying Gentoo patches ..."
 	# These two only needed when attempting to install outside build dir via
@@ -89,10 +93,6 @@ src_unpack() {
 	einfo "Done." # done applying Gentoo patches
 	echo
 
-	# glibc-2.10 getline fix
-#	sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
-#	ccp_patch "${FILESDIR}"/${PV}-glibc2.10.patch
-
 	gnuconfig_update
 }
 
@@ -148,13 +148,9 @@ src_compile() {
 
 	# Fix linking
 	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-#	export SHARE_LIB="\
-#		ld -shared -soname libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-#		ld -shared -soname libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-#		ld -shared -soname libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
+		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
 
 	# Can't use econf, configure rejects unknown options like --prefix
 	./configure \
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild.save b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild.save
deleted file mode 100644
index 7cc458e59..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild.save
+++ /dev/null
@@ -1,221 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-#	${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
-#	http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
-	virtual/blas
-	=sci-libs/fftw-2*
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.0.99
-	sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-#	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# glibc-2.10 getline fix
-#	sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
-#	ccp_patch "${FILESDIR}"/${PV}-glibc2.10.patch
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	userldflags="${LDFLAGS}"
-	export SHARED_LIB_FLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-#	export CCP4_SCR="${T}"
-
-	# Fix linking
-	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-#	export SHARE_LIB="\
-#		ld -shared -soname libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-#		ld -shared -soname libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-#		ld -shared -soname libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file} || die
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file} || die
-		fi
-	done
-
-	# Bins
-	dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
-	newbin bin/superpose superpose-ccp4 || die
-
-	# Fix libdir in all *.la files
-	sed -i \
-		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
-		"${D}"/usr/$(get_libdir)/*.la
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-
-	# Include files
-	insinto /usr/include
-	for i in ccp4 mmdb; do
-		doins -r "${S}"/include/${i} || die
-	done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}